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- PDB-5thw: Crystal structure of Amidase, hydantoinase/carbamoylase family fr... -

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Basic information

Entry
Database: PDB / ID: 5thw
TitleCrystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia multivorans
ComponentsDeacylase
KeywordsHYDROLASE / SSGCID / Burkholderia multivorans / N-carbamoyl-L-amino-acid hydrolase / Amidase / hydantoinase/carbamoylase family / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(AMINOCARBONYL)-BETA-ALANINE / Deacylase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia multivorans
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deacylase
B: Deacylase
C: Deacylase
D: Deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,57414
Polymers187,7934
Non-polymers78110
Water9,422523
1
A: Deacylase
B: Deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2877
Polymers93,8962
Non-polymers3905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-136 kcal/mol
Surface area27830 Å2
MethodPISA
2
C: Deacylase
D: Deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2877
Polymers93,8962
Non-polymers3905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-136 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.460, 88.510, 126.440
Angle α, β, γ (deg.)90.000, 90.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15:16 or (resid 17:18 and (name...
21(chain B and (resid 15:16 or (resid 17:18 and (name...
31(chain C and (resid 15:21 or (resid 22 and (name...
41(chain D and (resid 15:16 or (resid 17:18 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 15:16 or (resid 17:18 and (name...A15 - 16
121(chain A and (resid 15:16 or (resid 17:18 and (name...A17 - 18
131(chain A and (resid 15:16 or (resid 17:18 and (name...A14 - 503
141(chain A and (resid 15:16 or (resid 17:18 and (name...A14 - 503
151(chain A and (resid 15:16 or (resid 17:18 and (name...A14 - 503
161(chain A and (resid 15:16 or (resid 17:18 and (name...A14 - 503
211(chain B and (resid 15:16 or (resid 17:18 and (name...B15 - 16
221(chain B and (resid 15:16 or (resid 17:18 and (name...B17 - 18
231(chain B and (resid 15:16 or (resid 17:18 and (name...B15 - 504
241(chain B and (resid 15:16 or (resid 17:18 and (name...B15 - 504
251(chain B and (resid 15:16 or (resid 17:18 and (name...B15 - 504
261(chain B and (resid 15:16 or (resid 17:18 and (name...B15 - 504
311(chain C and (resid 15:21 or (resid 22 and (name...C15 - 21
321(chain C and (resid 15:21 or (resid 22 and (name...C22
331(chain C and (resid 15:21 or (resid 22 and (name...C14 - 503
341(chain C and (resid 15:21 or (resid 22 and (name...C14 - 503
351(chain C and (resid 15:21 or (resid 22 and (name...C14 - 503
361(chain C and (resid 15:21 or (resid 22 and (name...C14 - 503
411(chain D and (resid 15:16 or (resid 17:18 and (name...D15 - 16
421(chain D and (resid 15:16 or (resid 17:18 and (name...D17 - 18
431(chain D and (resid 15:16 or (resid 17:18 and (name...D15 - 504
441(chain D and (resid 15:16 or (resid 17:18 and (name...D15 - 504
451(chain D and (resid 15:16 or (resid 17:18 and (name...D15 - 504
461(chain D and (resid 15:16 or (resid 17:18 and (name...D15 - 504

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Components

#1: Protein
Deacylase


Mass: 46948.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: BMULJ_06149 / Plasmid: BumuA.12445.e.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3KRF1, N-carbamoyl-L-amino-acid hydrolase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-URP / N-(AMINOCARBONYL)-BETA-ALANINE / N-CARBAMYL-BETA-ALANINE / BETA-UREIDOPROPIONATE


Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Mosaicity: 0.305 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG+ screen, B2: 25% PEG 3350, 200mM Sodium thiocyanate; BumuA.12245.e.B1.PW37879 at 19.5mg/ml; cryo: 20% EG; tray 272537b2, puck ujd4-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 8, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 65364 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.86 % / Biso Wilson estimate: 37.33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.21
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.560.4942.890.82198.2
2.56-2.640.4593.150.834198.2
2.64-2.710.36440.904198.3
2.71-2.80.3024.710.92198.4
2.8-2.890.2485.670.945198.5
2.89-2.990.1967.240.965198.5
2.99-3.10.1568.710.975198.7
3.1-3.230.13210.230.981198.8
3.23-3.370.09913.140.99198.7
3.37-3.540.07716.440.994198.9
3.54-3.730.06618.950.995198.9
3.73-3.950.05322.070.996199
3.95-4.230.04625.210.997199
4.23-4.560.0427.930.998199.1
4.56-50.03630.110.998199.1
5-5.590.03927.980.998199.4
5.59-6.460.04127.380.998198.9
6.46-7.910.03330.770.998198.8
7.91-11.180.02637.20.999198.9
11.180.02438.790.999194.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PHENIX(1.11rc1_2513: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5I4M

5i4m


Resolution: 2.5→39.394 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2083 3.19 %0
Rwork0.1546 ---
obs0.1564 65358 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.41 Å2 / Biso mean: 45.0811 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: final / Resolution: 2.5→39.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12302 0 32 525 12859
Biso mean--46.78 39.7 -
Num. residues----1647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512674
X-RAY DIFFRACTIONf_angle_d0.73517259
X-RAY DIFFRACTIONf_chiral_restr0.0511926
X-RAY DIFFRACTIONf_plane_restr0.0062311
X-RAY DIFFRACTIONf_dihedral_angle_d17.467522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7302X-RAY DIFFRACTION10.889TORSIONAL
12B7302X-RAY DIFFRACTION10.889TORSIONAL
13C7302X-RAY DIFFRACTION10.889TORSIONAL
14D7302X-RAY DIFFRACTION10.889TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.55820.27461380.21614201433998
2.5582-2.62220.27261350.20764189432498
2.6222-2.6930.25191510.20164172432398
2.693-2.77230.26971600.19534139429998
2.7723-2.86170.28971550.19944197435299
2.8617-2.9640.24481790.1864138431799
2.964-3.08260.27241040.17634245434999
3.0826-3.22280.2281300.17914179430999
3.2228-3.39260.24841510.17814221437299
3.3926-3.60510.19321540.15694212436699
3.6051-3.88320.20141000.14634237433799
3.8832-4.27360.17641400.13194257439799
4.2736-4.8910.16351350.11414250438599
4.891-6.15830.18561400.12934289442999
6.1583-39.39910.17061110.13014349446098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2857-1.0282-2.5332.78151.60185.3377-0.0055-0.9019-0.16610.50290.008-0.06780.1951-0.2759-0.00270.386-0.0598-0.00680.69840.02830.38377.7384-15.639818.4967
21.5486-0.2223-0.48181.3474-0.57172.3560.0412-0.36810.11250.33330.05450.1749-0.2848-0.3875-0.10330.31940.00740.04640.5554-0.03320.32523.4392-4.466610.9411
31.37920.3080.03561.6907-1.35261.14690.13350.01970.48630.24540.09270.4489-0.394-0.7511-0.24460.38140.16050.07190.53520.02060.46591.28757.2186-0.0536
41.49390.4474-0.37621.2961-1.20672.18540.1538-0.42090.03430.4742-0.2012-0.231-0.51180.19860.06340.427-0.0649-0.05740.4051-0.06240.324920.97450.79698.5982
50.73550.2236-0.76170.99170.23632.0941-0.16260.16690.03180.0432-0.11350.1608-0.26170.39740.3430.2901-0.0496-0.04060.32790.04440.420429.73174.0008-21.895
61.26990.3167-0.55281.20090.30214.26190.0066-0.10980.21390.0851-0.14440.0196-0.3087-0.01180.14550.279-0.0597-0.04940.25680.01850.36726.07866.1794-11.4327
71.60230.0041-0.65411.41060.32052.57640.3003-0.59950.25950.705-0.08860.0372-0.84760.0032-0.1650.4168-0.1107-0.05730.4927-0.09830.328820.08566.75510.6964
82.677-0.386-0.57532.2966-1.50091.5831-0.0125-0.46710.03270.5939-0.1737-0.2858-0.24390.24690.21140.3548-0.0435-0.0650.4585-0.01240.295519.2092-3.313512.566
94.6657-3.9918-2.16177.93362.37223.3071-0.5225-1.17160.32571.45960.5351-0.4477-0.13240.30190.03340.5635-0.0311-0.08240.8555-0.05130.311911.6518-4.564325.1587
101.4345-0.40820.14472.71840.31251.6477-0.0488-0.05280.10920.2091-0.02190.2101-0.1594-0.09560.04630.2532-0.0155-0.01960.2092-0.00370.274710.4679-7.1889-56.6115
110.93740.07170.3042.10040.45291.36670.0126-0.0036-0.03990.17440.00630.13960.05730.02280.01810.27380.01710.01530.2183-0.01390.278216.1715-13.4157-53.3797
120.82520.0275-0.23770.18910.27412.2679-0.0637-0.0369-0.01690.009-0.0135-0.03170.21530.09690.0360.206-0.02050.01490.21550.01960.319231.0442-7.1306-27.6419
131.4062-0.94011.35735.2282-0.24941.4602-0.192-0.1830.15030.27360.16040.0839-0.2130.03270.13350.2918-0.0650.00770.3144-0.00350.295424.5768-1.7864-49.3421
144.13490.4599-0.40662.412.48686.98770.32050.32550.1107-0.4826-0.0339-0.5062-0.60890.2933-0.23370.3099-0.10080.01320.24570.09530.317924.2391-0.5582-63.8688
153.29451.35181.45044.2018-0.23725.8845-0.36510.36260.4791-0.53320.21920.0797-0.4224-0.6081-0.07270.3179-0.0612-0.09480.51360.13250.4771-35.51778.487913.8282
161.76440.45920.62521.5522-0.57421.8551-0.09030.2126-0.0736-0.33710.34190.29180.2821-0.6206-0.19960.3744-0.1145-0.09330.66850.02710.3746-40.4303-6.132124.1805
171.2992-0.15120.58221.0179-0.11431.8513-0.01390.1281-0.2011-0.16160.0078-0.08980.365-0.06130.02790.2944-0.01660.02890.2026-0.03440.3553-17.6933-10.594440.2934
181.696-0.30891.16471.87710.0773.60950.25620.5201-0.3446-0.69340.1809-0.0240.75330.0137-0.33280.463-0.01420.02970.3778-0.16590.383-23.2245-14.366522.3031
191.8520.43990.42212.0971-0.62681.8148-0.27420.57830.0546-0.54420.158-0.13890.2891-0.19020.12890.4499-0.07710.05460.6102-0.0630.3203-26.586-3.806615.1582
201.91670.2597-0.8732.672-0.82581.7390.03480.0467-0.00340.09710.12810.2332-0.0627-0.1023-0.1470.2713-0.00790.02970.29840.02320.2583-31.70075.972787.4157
210.89450.038-0.43280.35610.41191.5537-0.0288-0.1491-0.09930.04310.0329-0.0432-0.03190.1555-0.00740.2710.0386-0.04180.2525-0.00560.351-13.35610.391164.5024
222.52520.1518-1.87366.17970.38382.0815-0.187-0.0645-0.1813-0.0477-0.0431-0.02780.19870.16210.20510.24970.0299-0.01530.35320.08460.3106-21.6753-5.455588.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 33 )A14 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 150 )A34 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 195 )A151 - 195
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 234 )A196 - 234
5X-RAY DIFFRACTION5chain 'A' and (resid 235 through 269 )A235 - 269
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 326 )A270 - 326
7X-RAY DIFFRACTION7chain 'A' and (resid 327 through 358 )A327 - 358
8X-RAY DIFFRACTION8chain 'A' and (resid 359 through 402 )A359 - 402
9X-RAY DIFFRACTION9chain 'A' and (resid 403 through 425 )A403 - 425
10X-RAY DIFFRACTION10chain 'B' and (resid 15 through 108 )B15 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 212 )B109 - 212
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 358 )B213 - 358
13X-RAY DIFFRACTION13chain 'B' and (resid 359 through 402 )B359 - 402
14X-RAY DIFFRACTION14chain 'B' and (resid 403 through 426 )B403 - 426
15X-RAY DIFFRACTION15chain 'C' and (resid 14 through 33 )C14 - 33
16X-RAY DIFFRACTION16chain 'C' and (resid 34 through 195 )C34 - 195
17X-RAY DIFFRACTION17chain 'C' and (resid 196 through 326 )C196 - 326
18X-RAY DIFFRACTION18chain 'C' and (resid 327 through 358 )C327 - 358
19X-RAY DIFFRACTION19chain 'C' and (resid 359 through 425 )C359 - 425
20X-RAY DIFFRACTION20chain 'D' and (resid 15 through 195 )D15 - 195
21X-RAY DIFFRACTION21chain 'D' and (resid 196 through 378 )D196 - 378
22X-RAY DIFFRACTION22chain 'D' and (resid 379 through 425 )D379 - 425

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